Copy Number
The putative cancer-associated PDGs driven by SCNAs in each cancer type were identified by four criteria: 1) located in a peak region of a significantly recurrent focal SNCA locus estimated by the genomic identification of significant targets in cancer (GISTIC2) algorithm, (q≤0.25); 2) altered with high frequency and large amplitude (G-score ≥0.1); 3) mRNA reliably detected in at least 10% of tumor specimens in the given cancer type (90th percentile of FPKM value ≥1); and 4) mRNA significantly and positively correlated with copy numbers (Pearson P-value less than 0.001).
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| KIRC | KIRP | KICH | PRAD | BLCA | THYM | MESO | LUAD | LUSC | HNSC | ESCA | STAD | COAD | READ | PAAD | LIHC | CHOL | ACC | PCPG | THCA | BRCA | OV | CESC | UCEC | UCS | SARC | TGCT | LAML | DLBC | LGG | GBM | UVM | SKCM | |||||||||||||||||||||||||||||||||||
| HGNC Symbol | Ensembl Gene ID | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del |
| HLCS | ENSG00000159267 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.02 | 0.05 | 0.03 | 0.04 | 0.03 | 0.09 | 0.03 | 0.05 | 0.02 | 0.02 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.12 | 0.09 | 0.13 | 0.01 | 0.04 | 0.01 | 0.11 | 0.03 | 0.08 | 0.07 | 0.04 | 0.00 | 0.11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 |
| SLC39A5 | ENSG00000139540 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.01 | 0.04 | 0.01 | 0.01 | 0.02 | 0.10 | 0.04 | 0.09 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.06 | 0.01 | 0.00 | 0.01 | 0.28 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.25 | 0.04 | 0.04 | 0.00 | 0.15 | 0.00 | 0.55 | 0.04 | 0.15 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.03 | 0.05 | 0.05 | 0.00 | 0.00 | 0.07 | 0.03 |
| ULK4 | ENSG00000168038 | 0.00 | 0.18 | 0.00 | 0.05 | 0.08 | 0.00 | 0.01 | 0.01 | 0.07 | 0.08 | 0.00 | 0.03 | 0.01 | 0.38 | 0.02 | 0.04 | 0.02 | 0.08 | 0.00 | 0.07 | 0.05 | 0.04 | 0.08 | 0.08 | 0.00 | 0.03 | 0.04 | 0.04 | 0.01 | 0.03 | 0.05 | 0.04 | 0.00 | 0.20 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.12 | 0.09 | 0.17 | 0.02 | 0.08 | 0.03 | 0.06 | 0.03 | 0.22 | 0.08 | 0.11 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.07 | 0.01 | 0.04 | 0.01 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 |
| PLD2 | ENSG00000129219 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.02 | 0.02 | 0.02 | 0.03 | 0.05 | 0.05 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.12 | 0.02 | 0.03 | 0.02 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.05 | 0.12 | 0.06 | 0.01 | 0.03 | 0.04 | 0.03 | 0.13 | 0.12 | 0.17 | 0.25 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.03 |
| NELL2 | ENSG00000184613 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.06 | 0.04 | 0.00 | 0.00 | 0.01 | 0.05 | 0.05 | 0.04 | 0.08 | 0.02 | 0.02 | 0.03 | 0.10 | 0.06 | 0.07 | 0.05 | 0.02 | 0.00 | 0.07 | 0.04 | 0.00 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.13 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.05 | 0.27 | 0.07 | 0.03 | 0.01 | 0.06 | 0.01 | 0.51 | 0.08 | 0.17 | 0.10 | 0.00 | 0.02 | 0.00 | 0.01 | 0.13 | 0.00 | 0.03 | 0.05 | 0.04 | 0.07 | 0.00 | 0.00 | 0.06 | 0.06 |
| GPR61 | ENSG00000156097 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.33 | 0.01 | 0.13 | 0.01 | 0.13 | 0.00 | 0.12 | 0.06 | 0.12 | 0.03 | 0.07 | 0.00 | 0.06 | 0.00 | 0.07 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.26 | 0.00 | 0.00 | 0.05 | 0.10 | 0.17 | 0.15 | 0.01 | 0.08 | 0.03 | 0.03 | 0.08 | 0.06 | 0.05 | 0.10 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.07 | 0.10 |
| GSK3A | ENSG00000105723 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.09 | 0.14 | 0.03 | 0.00 | 0.00 | 0.05 | 0.04 | 0.09 | 0.04 | 0.13 | 0.07 | 0.01 | 0.02 | 0.02 | 0.06 | 0.04 | 0.03 | 0.02 | 0.02 | 0.01 | 0.02 | 0.02 | 0.03 | 0.02 | 0.03 | 0.12 | 0.01 | 0.05 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.17 | 0.27 | 0.11 | 0.05 | 0.05 | 0.04 | 0.09 | 0.17 | 0.19 | 0.12 | 0.00 | 0.04 | 0.01 | 0.00 | 0.10 | 0.13 | 0.01 | 0.11 | 0.03 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| COL25A1 | ENSG00000188517 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.04 | 0.03 | 0.05 | 0.01 | 0.02 | 0.03 | 0.07 | 0.02 | 0.05 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.01 | 0.01 | 0.09 | 0.00 | 0.11 | 0.12 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.04 | 0.27 | 0.01 | 0.02 | 0.01 | 0.05 | 0.00 | 0.18 | 0.09 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 |
| RPS6KB2 | ENSG00000175634 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.10 | 0.00 | 0.22 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.15 | 0.01 | 0.18 | 0.02 | 0.43 | 0.01 | 0.40 | 0.02 | 0.16 | 0.02 | 0.01 | 0.01 | 0.05 | 0.02 | 0.02 | 0.01 | 0.14 | 0.01 | 0.20 | 0.02 | 0.08 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.50 | 0.03 | 0.29 | 0.03 | 0.24 | 0.00 | 0.18 | 0.02 | 0.29 | 0.02 | 0.13 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.19 | 0.02 |
| KCNJ2 | ENSG00000123700 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.24 | 0.01 | 0.02 | 0.00 | 0.13 | 0.00 | 0.17 | 0.00 | 0.20 | 0.00 | 0.07 | 0.02 | 0.24 | 0.03 | 0.11 | 0.03 | 0.05 | 0.01 | 0.06 | 0.05 | 0.05 | 0.10 | 0.22 | 0.01 | 0.12 | 0.01 | 0.14 | 0.06 | 0.02 | 0.01 | 0.00 | 0.00 | 0.41 | 0.02 | 0.26 | 0.03 | 0.15 | 0.03 | 0.10 | 0.02 | 0.34 | 0.02 | 0.23 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.03 | 0.01 | 0.17 | 0.01 | 0.23 | 0.01 |
| CES2 | ENSG00000172831 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.06 | 0.11 | 0.03 | 0.00 | 0.00 | 0.03 | 0.06 | 0.05 | 0.02 | 0.05 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.04 | 0.05 | 0.01 | 0.23 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.05 | 0.30 | 0.03 | 0.04 | 0.04 | 0.07 | 0.10 | 0.14 | 0.03 | 0.04 | 0.15 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.04 | 0.01 |
| ZRANB1 | ENSG00000019995 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.06 | 0.03 | 0.12 | 0.00 | 0.02 | 0.02 | 0.17 | 0.04 | 0.03 | 0.05 | 0.06 | 0.02 | 0.03 | 0.10 | 0.05 | 0.15 | 0.08 | 0.01 | 0.07 | 0.01 | 0.06 | 0.03 | 0.01 | 0.02 | 0.10 | 0.14 | 0.11 | 0.11 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.10 | 0.28 | 0.21 | 0.02 | 0.05 | 0.06 | 0.07 | 0.10 | 0.04 | 0.07 | 0.07 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.13 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.04 |
| KIAA0195 | ENSG00000177728 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.21 | 0.00 | 0.02 | 0.01 | 0.09 | 0.02 | 0.17 | 0.01 | 0.25 | 0.02 | 0.10 | 0.03 | 0.33 | 0.06 | 0.13 | 0.03 | 0.03 | 0.01 | 0.05 | 0.02 | 0.05 | 0.10 | 0.26 | 0.00 | 0.08 | 0.01 | 0.13 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.38 | 0.03 | 0.37 | 0.03 | 0.24 | 0.02 | 0.23 | 0.01 | 0.79 | 0.00 | 0.25 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.09 | 0.01 | 0.14 | 0.01 | 0.25 | 0.02 |
| GABRB3 | ENSG00000166206 | 0.01 | 0.01 | 0.00 | 0.02 | 0.14 | 0.00 | 0.03 | 0.04 | 0.10 | 0.11 | 0.00 | 0.00 | 0.00 | 0.22 | 0.02 | 0.12 | 0.06 | 0.11 | 0.06 | 0.04 | 0.11 | 0.10 | 0.01 | 0.09 | 0.01 | 0.09 | 0.01 | 0.04 | 0.00 | 0.04 | 0.01 | 0.04 | 0.00 | 0.04 | 0.17 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.12 | 0.08 | 0.29 | 0.06 | 0.05 | 0.02 | 0.07 | 0.13 | 0.43 | 0.09 | 0.11 | 0.04 | 0.03 | 0.04 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.00 | 0.04 | 0.10 |
| SLC38A7 | ENSG00000103042 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.03 | 0.01 | 0.03 | 0.02 | 0.10 | 0.01 | 0.02 | 0.03 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.09 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.04 | 0.05 | 0.15 | 0.00 | 0.06 | 0.02 | 0.07 | 0.00 | 0.16 | 0.03 | 0.06 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 | 0.04 |
| HPN | ENSG00000105707 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.18 | 0.02 | 0.00 | 0.00 | 0.11 | 0.02 | 0.26 | 0.00 | 0.41 | 0.02 | 0.08 | 0.01 | 0.22 | 0.04 | 0.12 | 0.04 | 0.07 | 0.00 | 0.04 | 0.01 | 0.11 | 0.01 | 0.07 | 0.02 | 0.13 | 0.03 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.15 | 0.01 | 0.70 | 0.04 | 0.17 | 0.02 | 0.19 | 0.01 | 1.44 | 0.00 | 0.28 | 0.05 | 0.01 | 0.02 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.06 | 0.01 |
| DSTYK | ENSG00000133059 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.05 | 0.02 | 0.00 | 0.12 | 0.00 | 0.15 | 0.01 | 0.11 | 0.01 | 0.05 | 0.00 | 0.16 | 0.06 | 0.05 | 0.01 | 0.04 | 0.00 | 0.12 | 0.02 | 0.00 | 0.00 | 0.21 | 0.01 | 0.18 | 0.02 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.29 | 0.08 | 0.07 | 0.00 | 0.12 | 0.01 | 0.16 | 0.00 | 0.10 | 0.15 | 0.05 | 0.02 | 0.01 | 0.00 | 0.26 | 0.02 | 0.08 | 0.01 | 0.33 | 0.01 | 0.09 | 0.00 | 0.20 | 0.01 |
| SETMAR | ENSG00000170364 | 0.00 | 0.18 | 0.00 | 0.02 | 0.07 | 0.00 | 0.01 | 0.04 | 0.25 | 0.06 | 0.00 | 0.05 | 0.04 | 0.13 | 0.03 | 0.04 | 0.03 | 0.09 | 0.03 | 0.05 | 0.03 | 0.20 | 0.03 | 0.14 | 0.00 | 0.06 | 0.01 | 0.09 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.18 | 0.06 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.14 | 0.04 | 0.12 | 0.25 | 0.03 | 0.02 | 0.04 | 0.04 | 0.05 | 0.21 | 0.20 | 0.05 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 |
| CP | ENSG00000047457 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.10 | 0.01 | 0.80 | 0.01 | 0.42 | 0.00 | 0.54 | 0.03 | 0.14 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.10 | 0.01 | 0.03 | 0.03 | 0.09 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.15 | 0.01 | 0.67 | 0.02 | 0.40 | 0.01 | 0.15 | 0.01 | 0.24 | 0.02 | 0.08 | 0.07 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.04 | 0.04 |
| TDP2 | ENSG00000111802 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.39 | 0.02 | 0.00 | 0.01 | 0.01 | 0.03 | 0.06 | 0.02 | 0.08 | 0.06 | 0.02 | 0.05 | 0.16 | 0.11 | 0.05 | 0.06 | 0.04 | 0.03 | 0.02 | 0.03 | 0.03 | 0.04 | 0.12 | 0.01 | 0.06 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.03 | 0.39 | 0.05 | 0.09 | 0.05 | 0.06 | 0.02 | 0.20 | 0.02 | 0.04 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.02 | 0.03 | 0.01 | 0.18 | 0.00 | 0.15 | 0.01 |
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